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Matplotlib figures are not shown on the compiled documentation. #788

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Vital-Fernandez opened this issue Apr 18, 2024 · 4 comments
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@Vital-Fernandez
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Hi I have been using nbsphinx for a couple of years for my library to compile the tutorials from notebooks.

I had to reinstall python and now the figures are not longer showed on the sphinx documentation (they show fine on the jupyter notebooks with %matplotlib widget).

If I run the command:

python -c "import sys; print('\n',sys.version); import ipympl; print('ipympl version:', ipympl.__version__)" && jupyter --version && jupyter nbextension list && jupyter labextension list

I get

ipympl version: 0.9.3
Selected Jupyter core packages...
IPython : 8.23.0
ipykernel : 6.29.4
ipywidgets : 8.1.2
jupyter_client : 8.6.1
jupyter_core : 5.7.2
jupyter_server : 2.13.0
jupyterlab : 4.1.6
nbclient : 0.10.0
nbconvert : 7.16.3
nbformat : 5.10.4
notebook : 7.1.2
qtconsole : 5.5.1
traitlets : 5.14.2
Known nbextensions:
config dir: /home/vital/anaconda3/etc/jupyter/nbconfig
notebook section
jupyter-matplotlib/extension enabled
- Validating: OK
nbextensions_configurator/config_menu/main enabled
- Validating: problems found:
- require? X nbextensions_configurator/config_menu/main
jupyterlab-plotly/extension enabled
- Validating: OK
pydeck/extension enabled
- Validating: problems found:
- require? X pydeck/extension
jupyter-js-widgets/extension enabled
- Validating: OK
contrib_nbextensions_help_item/main enabled
- Validating: OK
tree section
nbextensions_configurator/tree_tab/main enabled
- Validating: problems found:
- require? X nbextensions_configurator/tree_tab/main
JupyterLab v4.1.6
/home/vital/PycharmProjects/lime/venv/share/jupyter/labextensions
jupyter-matplotlib v0.11.3 enabled OK
jupyterlab_pygments v0.3.0 enabled OK (python, jupyterlab_pygments)
@jupyter-widgets/jupyterlab-manager v5.0.10 enabled OK (python, jupyterlab_widgets)
@jupyter-notebook/lab-extension v7.1.2 enabled OK

I am using ubuntu 22.04.04 with python 3.11 and these are some of the packages I have installed:

docutils 0.20.1
ipympl 0.9.3
ipython 8.23.0
jupyter 1.0.0
jupyter_client 8.6.1
jupyter-console 6.6.3
jupyter-contrib-core 0.4.2
jupyter-contrib-nbextensions 0.7.0
jupyter_core 5.7.2
jupyter-events 0.10.0
jupyter-highlight-selected-word 0.2.0
jupyter-lsp 2.2.5
jupyter-nbextensions-configurator 0.6.3
jupyter_server 2.13.0
jupyter_server_terminals 0.5.3
jupyterlab 4.1.6
jupyterlab_pygments 0.3.0
jupyterlab_server 2.26.0
jupyterlab_widgets 3.0.10
matplotlib 3.7.2
matplotlib-inline 0.1.6
mplcursors 0.5.2
nbclient 0.10.0
nbconvert 7.16.3
nbformat 5.10.4
nbsphinx 0.9.2
notebook 7.1.2
notebook_shim 0.2.4
numpy 1.24.4
pip 24.0
scipy 1.10.1
Sphinx 7.2.6
sphinx-rtd-theme 2.0.0
sphinxcontrib-applehelp 1.0.8
sphinxcontrib-devhelp 1.0.6
sphinxcontrib-htmlhelp 2.0.5
sphinxcontrib-jquery 4.1
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.7
sphinxcontrib-serializinghtml 1.1.10

Thank you very much for any advice.

@mgeier
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mgeier commented May 5, 2024

Thanks for the report, can you please provide a minimal reproducible example?

I don't have any experience with the widget backend, I assume it worked before your re-installation?

@mgeier
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mgeier commented May 5, 2024

I have created #794 to test this, and it seems to work. What is different in your case?

@vincefn
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vincefn commented May 25, 2024

Hi @mgeier - I'm facing the same issue. I have attached a zip file with
an example pre-processed notebook, the conf.py and index.rst to reproduce this, and the html produced directly by nbconvert.

Notes:

  • this happens only when the notebook is already rendered - if I let nbsphinx render the notebook, then the figure appears correctly
  • nbconvert correctly renders the page with the figure (using jupyter nbconvert --to html ipympl-lab-test.ipynb)
  • if you open the notebook in jupyter-lab, you'll probably see it it does not show the png rendering (instead Error displaying widget: model not found) - some issue in jupyter-lab not using the embedded png as an alternate representation of the graph. Since nbconvert works I expect it should also work with nbsphinx

The minimal test environment was created using mambaforge with just mamba create -n ipympl-lab python=3.12 ipympl matplotlib jupyterlab sphinx nbsphinx.

Here's the full list of the environment (here on a mac):

(ipympl-lab) vincent@vincent tmp % jupyter --version
Selected Jupyter core packages...
IPython          : 8.24.0
ipykernel        : 6.29.3
ipywidgets       : 8.1.2
jupyter_client   : 8.6.2
jupyter_core     : 5.7.2
jupyter_server   : 2.14.0
jupyterlab       : 4.2.1
nbclient         : 0.10.0
nbconvert        : 7.16.4
nbformat         : 5.10.4
notebook         : not installed
qtconsole        : not installed
traitlets        : 5.14.3
(ipympl-lab) vincent@vincent tmp % jupyter labextension list
JupyterLab v4.2.1
/Users/vincent/mambaforge/envs/ipympl-lab/share/jupyter/labextensions
        jupyterlab_pygments v0.3.0 enabled OK (python, jupyterlab_pygments)
        jupyter-matplotlib v0.11.4 enabled OK
        @jupyter-widgets/jupyterlab-manager v5.0.10 enabled OK (python, jupyterlab_widgets)

(ipympl-lab) vincent@vincent tmp % conda list
# packages in environment at /Users/vincent/mambaforge/envs/ipympl-lab:
#
# Name                    Version                   Build  Channel
alabaster                 0.7.16             pyhd8ed1ab_0    conda-forge
anyio                     4.3.0              pyhd8ed1ab_0    conda-forge
appnope                   0.1.4              pyhd8ed1ab_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py312h02f2b3b_4    conda-forge
arrow                     1.3.0              pyhd8ed1ab_0    conda-forge
asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge
async-lru                 2.0.4              pyhd8ed1ab_0    conda-forge
attrs                     23.2.0             pyh71513ae_0    conda-forge
babel                     2.14.0             pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.3             pyha770c72_0    conda-forge
bleach                    6.1.0              pyhd8ed1ab_0    conda-forge
brotli                    1.1.0                hb547adb_1    conda-forge
brotli-bin                1.1.0                hb547adb_1    conda-forge
brotli-python             1.1.0           py312h9f69965_1    conda-forge
bzip2                     1.0.8                h93a5062_5    conda-forge
ca-certificates           2024.2.2             hf0a4a13_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
certifi                   2024.2.2           pyhd8ed1ab_0    conda-forge
cffi                      1.16.0          py312h8e38eb3_0    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.2.2              pyhd8ed1ab_0    conda-forge
contourpy                 1.2.1           py312h0fef576_0    conda-forge
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
debugpy                   1.8.1           py312h20a0b95_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
docutils                  0.21.2             pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
exceptiongroup            1.2.0              pyhd8ed1ab_2    conda-forge
executing                 2.0.1              pyhd8ed1ab_0    conda-forge
fonttools                 4.52.1          py312h7e5086c_0    conda-forge
fqdn                      1.5.1              pyhd8ed1ab_0    conda-forge
freetype                  2.12.1               hadb7bae_2    conda-forge
h11                       0.14.0             pyhd8ed1ab_0    conda-forge
h2                        4.1.0              pyhd8ed1ab_0    conda-forge
hpack                     4.0.0              pyh9f0ad1d_0    conda-forge
httpcore                  1.0.5              pyhd8ed1ab_0    conda-forge
httpx                     0.27.0             pyhd8ed1ab_0    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_0    conda-forge
idna                      3.7                pyhd8ed1ab_0    conda-forge
imagesize                 1.4.1              pyhd8ed1ab_0    conda-forge
importlib-metadata        7.1.0              pyha770c72_0    conda-forge
importlib_metadata        7.1.0                hd8ed1ab_0    conda-forge
importlib_resources       6.4.0              pyhd8ed1ab_0    conda-forge
ipykernel                 6.29.3             pyh3cd1d5f_0    conda-forge
ipympl                    0.9.4              pyhd8ed1ab_0    conda-forge
ipython                   8.24.0             pyh707e725_0    conda-forge
ipython_genutils          0.2.0              pyhd8ed1ab_1    conda-forge
ipywidgets                8.1.2              pyhd8ed1ab_1    conda-forge
isoduration               20.11.0            pyhd8ed1ab_0    conda-forge
jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.4              pyhd8ed1ab_0    conda-forge
json5                     0.9.25             pyhd8ed1ab_0    conda-forge
jsonpointer               2.4             py312h81bd7bf_3    conda-forge
jsonschema                4.22.0             pyhd8ed1ab_0    conda-forge
jsonschema-specifications 2023.12.1          pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.22.0             pyhd8ed1ab_0    conda-forge
jupyter-lsp               2.2.5              pyhd8ed1ab_0    conda-forge
jupyter_client            8.6.2              pyhd8ed1ab_0    conda-forge
jupyter_core              5.7.2           py312h81bd7bf_0    conda-forge
jupyter_events            0.10.0             pyhd8ed1ab_0    conda-forge
jupyter_server            2.14.0             pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.5.3              pyhd8ed1ab_0    conda-forge
jupyterlab                4.2.1              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.3.0              pyhd8ed1ab_1    conda-forge
jupyterlab_server         2.27.2             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.10             pyhd8ed1ab_0    conda-forge
kiwisolver                1.4.5           py312h389731b_1    conda-forge
krb5                      1.21.2               h92f50d5_0    conda-forge
lcms2                     2.16                 ha0e7c42_0    conda-forge
lerc                      4.0.0                h9a09cb3_0    conda-forge
libblas                   3.9.0           22_osxarm64_openblas    conda-forge
libbrotlicommon           1.1.0                hb547adb_1    conda-forge
libbrotlidec              1.1.0                hb547adb_1    conda-forge
libbrotlienc              1.1.0                hb547adb_1    conda-forge
libcblas                  3.9.0           22_osxarm64_openblas    conda-forge
libcxx                    17.0.6               h5f092b4_0    conda-forge
libdeflate                1.20                 h93a5062_0    conda-forge
libedit                   3.1.20191231         hc8eb9b7_2    conda-forge
libexpat                  2.6.2                hebf3989_0    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libgfortran               5.0.0           13_2_0_hd922786_3    conda-forge
libgfortran5              13.2.0               hf226fd6_3    conda-forge
libjpeg-turbo             3.0.0                hb547adb_1    conda-forge
liblapack                 3.9.0           22_osxarm64_openblas    conda-forge
libopenblas               0.3.27          openmp_h6c19121_0    conda-forge
libpng                    1.6.43               h091b4b1_0    conda-forge
libsodium                 1.0.18               h27ca646_1    conda-forge
libsqlite                 3.45.3               h091b4b1_0    conda-forge
libtiff                   4.6.0                h07db509_3    conda-forge
libwebp-base              1.4.0                h93a5062_0    conda-forge
libxcb                    1.15                 hf346824_0    conda-forge
libzlib                   1.2.13               h53f4e23_5    conda-forge
llvm-openmp               18.1.5               hde57baf_0    conda-forge
markupsafe                2.1.5           py312he37b823_0    conda-forge
matplotlib                3.8.4           py312h1f38498_2    conda-forge
matplotlib-base           3.8.4           py312h4479663_2    conda-forge
matplotlib-inline         0.1.7              pyhd8ed1ab_0    conda-forge
mistune                   3.0.2              pyhd8ed1ab_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nbclient                  0.10.0             pyhd8ed1ab_0    conda-forge
nbconvert                 7.16.4               hd8ed1ab_0    conda-forge
nbconvert-core            7.16.4             pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.16.4               hd8ed1ab_0    conda-forge
nbformat                  5.10.4             pyhd8ed1ab_0    conda-forge
nbsphinx                  0.9.4              pyhd8ed1ab_0    conda-forge
ncurses                   6.5                  hb89a1cb_0    conda-forge
nest-asyncio              1.6.0              pyhd8ed1ab_0    conda-forge
notebook-shim             0.2.4              pyhd8ed1ab_0    conda-forge
numpy                     1.26.4          py312h8442bc7_0    conda-forge
openjpeg                  2.5.2                h9f1df11_0    conda-forge
openssl                   3.3.0                hfb2fe0b_3    conda-forge
overrides                 7.7.0              pyhd8ed1ab_0    conda-forge
packaging                 24.0               pyhd8ed1ab_0    conda-forge
pandoc                    3.2                  hce30654_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.4              pyhd8ed1ab_0    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    10.3.0          py312h8a801b1_0    conda-forge
pip                       24.0               pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              4.2.2              pyhd8ed1ab_0    conda-forge
prometheus_client         0.20.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.42             pyha770c72_0    conda-forge
psutil                    5.9.8           py312he37b823_0    conda-forge
pthread-stubs             0.4               h27ca646_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycparser                 2.22               pyhd8ed1ab_0    conda-forge
pygments                  2.18.0             pyhd8ed1ab_0    conda-forge
pyobjc-core               10.2            py312h9d22092_0    conda-forge
pyobjc-framework-cocoa    10.2            py312h9d22092_0    conda-forge
pyparsing                 3.1.2              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.12.3          h4a7b5fc_0_cpython    conda-forge
python-dateutil           2.9.0              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.19.1             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python_abi                3.12                    4_cp312    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.1           py312h02f2b3b_1    conda-forge
pyzmq                     26.0.3          py312hfa13136_0    conda-forge
readline                  8.2                  h92ec313_1    conda-forge
referencing               0.35.1             pyhd8ed1ab_0    conda-forge
requests                  2.32.2             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rpds-py                   0.18.1          py312h552d48e_0    conda-forge
send2trash                1.8.3              pyh31c8845_0    conda-forge
setuptools                70.0.0             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.1              pyhd8ed1ab_0    conda-forge
snowballstemmer           2.2.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
sphinx                    7.3.7              pyhd8ed1ab_0    conda-forge
sphinxcontrib-applehelp   1.0.8              pyhd8ed1ab_0    conda-forge
sphinxcontrib-devhelp     1.0.6              pyhd8ed1ab_0    conda-forge
sphinxcontrib-htmlhelp    2.0.5              pyhd8ed1ab_0    conda-forge
sphinxcontrib-jsmath      1.0.1              pyhd8ed1ab_0    conda-forge
sphinxcontrib-qthelp      1.0.7              pyhd8ed1ab_0    conda-forge
sphinxcontrib-serializinghtml 1.1.10             pyhd8ed1ab_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
terminado                 0.18.1             pyh31c8845_0    conda-forge
tinycss2                  1.3.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.13               h5083fa2_1    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.4             py312he37b823_0    conda-forge
traitlets                 5.14.3             pyhd8ed1ab_0    conda-forge
types-python-dateutil     2.9.0.20240316     pyhd8ed1ab_0    conda-forge
typing-extensions         4.11.0               hd8ed1ab_0    conda-forge
typing_extensions         4.11.0             pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2024a                h0c530f3_0    conda-forge
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   2.2.1              pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
webcolors                 1.13               pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
websocket-client          1.8.0              pyhd8ed1ab_0    conda-forge
wheel                     0.43.0             pyhd8ed1ab_1    conda-forge
widgetsnbextension        4.0.10             pyhd8ed1ab_0    conda-forge
xorg-libxau               1.0.11               hb547adb_0    conda-forge
xorg-libxdmcp             1.1.3                h27ca646_0    conda-forge
xz                        5.2.6                h57fd34a_0    conda-forge
yaml                      0.2.5                h3422bc3_2    conda-forge
zeromq                    4.3.5                hcc0f68c_4    conda-forge
zipp                      3.17.0             pyhd8ed1ab_0    conda-forge
zstd                      1.5.6                hb46c0d2_0    conda-forge

@vincefn
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vincefn commented May 25, 2024

A followup: after a few more tests, there is an option "save widget state automatically" in jupyter-lab:

image

Once this is activated this seems to change something in the saved processed notebook, and the rendering is then correct using both nbsphinx and nbconvert, and also when re-opening the notebook in jupyter-lab.

Maybe @Vital-Fernandez can confirm if this also solves the issue for him.

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